In her case, she was out of alignment with other ships. So in order to standardize her with the rest of the ships, a method was created to allow previous owners to retain her higher earning while newer players had the more standard rates.
Worth noting that the Combat Mission she has gives an extra +30% Credits, which is the equivalent of an additional flag. In some ways, that's not small, in other ways it's not large. Still, as an outlier, it was standardized before she was returned and available for purchase.
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Also worth noting. I wasn't around when she was available originally, but I've been told that she was strong in more areas then just her credit gain back at the time when she was available. The removal wasn't purely about credits back when it happened.
The game changed and those advantages became less pronounced as time wore on, so the concept of returning her had to address the remaining outlier in the ...
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